MolNFT v1 · #94555 · protein
Crystal structure of human arginase-2 complexed with inhibitor 14
4I06 · Arginase-2, mitochondrial: “Crystal structure of human arginase-2 complexed with inhibitor 14”. X-ray diffraction, 3 ligands (BEN, X8A, MN), 14 pockets (best druggability 0.80). MolNFT v1 #94555 on GenesisL1: 3D structure, binding…
- PDB
- 4I06
- Type
- protein
- Length
- 918 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase-2, mitochondrial
- EC
- 3.5.3.1
- UniProt
- P78540
- Ligands
- BEN, X8A, MN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase-2, mitochondrial (EC 3.5.3.1) | protein | 306 | 43% helix, 17% strand | P78540 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 3 copies · chains A, B, C
- X8A · [(5R)-5-carboxy-5-(methylamino)-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-) · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C
- BME · Beta-mercaptoethanol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.80 | 0.81 | 71 | empty |
| 2 | 110 | 0.50 | 0.82 | 24 | X8A |
| 3 | 79 | 0.44 | 0.81 | 20 | empty |
| 4 | 92 | 0.43 | 0.80 | 18 | X8A |
| 5 | 87 | 0.42 | 0.80 | 19 | X8A |
Interfaces
3 interfaces between chains.
- A–B · 678 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 678 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 671 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (additive adduct).
Compared structures
- 4I06 · Crystal structure of human Arginase-2 complexed with inhibitor 14 · the same entry in another collection · chain A against A, TM-score 1.00
- P78540 · AlphaFold monomer V2.0 prediction for arginase-2, mitochondrial (P78540) · a predicted model of the same protein · chain C against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P78540
- Elsewhere: RCSB PDB 4I06 · PDBe 4I06 · UniProt P78540
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